This article was recommended at a talk I attended. The thesis is that we need to look at the electronic health record from the bottom up.
George Hripcsak and David J Albers. Next-generation phenotyping of electronic health records. J Am Med Inform Assoc. 2013 Jan-Feb; 20(1): 117–121. Available in html format or pdf format.
You can find an earlier version of this page on my blog.